RetrogeneDB ID: retro_ttru_1145

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_105564:4..550(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SPOCK3
• Ensembl ID: ENSTTRG00000013385
• Aliases: None
• Description: sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3 [Source:HGNC Symbol;Acc:13565]

Sequence

>retro_ttru_1145
GACGATGATTATTTCCGCACTTGGAGTCCAGGGAAGGCCTTCGATGGGGCTCTAGACCCATGCTTAAGGCTGAAATGTAG
TCGCCACGAAGTGTGCATTATTCAAGGTTCTCAGACCGCAGTCTGCGTTGGTCAGCGGAGGCTCACGCACAGTATGAAAG
ATGCAGGAGTTGGGCATAAGCAGTGGAGGGGTCCTCCGACATCCACCTGCCAGCAGTGCTCGGGGGTCTCTACCAGCCCT
GTCTGTGGTTCAGATGGACATACCTACTCTTCTCAGTGCAAACTAGAATACCAGGCATGCATCTTAGGAATACAGATCTC
AGTCAAGTGCGAAGGATGTTGCCTGTGTCCTTCAGATACGACCATGGGCTCAAGCAGGAATATGAAGAGGGCCTGCAGTG
ACCTGGAGCTCAGGCAGATGGCCAGCAGACTGCTGGACTGGTTCAAGGCCCTGCATGAGAGTGGGGGCCAGAACAAGAAG
ACGAAAGCATCGCTGCGGACCGGAGAGAAGAAGATTTGATACCCGTATTTTGCCAATTGCAAGGAT

Alignment

ORF - retro_ttru_1145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.89 %
• Parental protein coverage: 50.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDDYFRTWSPGKAFDGALDPTKDPCLRLKCSRHEVCIVQGSQTAVCVGQRRLTHSMKDAGVGQKQWRGPP
          .DDYFRTWSPGKAFDGAL....DPCLRLKCSRHEVCI.QGSQTAVCVGQRRLTHSMKDAGVG.KQWRGPP
Retrocopy DDDYFRTWSPGKAFDGAL----DPCLRLKCSRHEVCIIQGSQTAVCVGQRRLTHSMKDAGVGHKQWRGPP

Parental  TSACQQCSGVSTSPVCGSDGHTYSSQCKLEYQACILGKQISVKCGGRCPCPSDTTAGSSRNMKRACSDLE
          TS.CQQCSGVSTSPVCGSDGHTYSSQCKLEYQACILG.QISVKC.G.C.CPSDTT.GSSRNMKRACSDLE
Retrocopy TSTCQQCSGVSTSPVCGSDGHTYSSQCKLEYQACILGIQISVKCEGCCLCPSDTTMGSSRNMKRACSDLE

Parental  LREMASRLRDWFKALHESGGQNKKTKASLR-PERSRFDTSILPI-CKD
          LR.MASRL.DWFKALHESGGQNKKTKASLR.PER.RFDT.ILPI.CKD
Retrocopy LRQMASRLLDWFKALHESGGQNKKTKASLR>PERRRFDTRILPI<CKD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1145 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1145 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tursiops truncatus	ENSTTRG00000013385	1 retrocopy	retro_ttru_1145 ,